Ligands and environments ‹ 5gak ‹ Protein Data Bank in Europe (PDBe)

1 bound ligand:

3HE 3401(1) Environment details ›

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/package.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/core.z.js

-- required by ClazzNode

Jmol JavaScript applet _PDBE_JMOL__824177999022228__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript true

AppletRegistry.checkIn(_PDBE_JMOL__824177999022228__)

vwrOptions:

{ "name":"_PDBE_JMOL","allowJavaScript":true,"applet":true,"documentBase":"https://www.ebi.ac.uk/pdbe/entry/pdb/5gak/ligands","platform":"J.awtjs2d.Platform","fullName":"_PDBE_JMOL__824177999022228__","progressbar":true,"codePath":"https://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/","display":"_PDBE_JMOL_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"824177999022228","progresscolor":"#66666","bgcolor":"#ffffff" }

setting document base to "https://www.ebi.ac.uk/pdbe/entry/pdb/5gak/ligands"

Jmol Version: 14.3.6_2014.08.17b 2014-08-17 17:24

java.vendor: Java2Script (HTML5)

java.version: JSmol 14.3.6_2014.08.14

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:_PDBE_JMOL (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #ffffff

backgroundColor = "#ffffff"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet _PDBE_JMOL__824177999022228__ ready

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/corescript.z.js

script 1 started

FileManager.getAtomSetCollectionFromFile(https://www.ebi.ac.uk/pdbe/entry-files/download/5gak.cif)

FileManager opening 1 https://www.ebi.ac.uk/pdbe/entry-files/download/5gak.cif

The Resolver thinks MMCif

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/adapter/readers/cif/MMCifReader.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/adapter/readers/cif/CifReader.js

-- required by J.adapter.readers.cif.MMCifReader

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/JU/CifDataParser.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/corebio.z.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/render/MeshRenderer.js

-- required by J.renderbio.BioShapeRenderer

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/shape/Mesh.js

TITLE: Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome.

Setting space group name to HM:P 1

found biomolecule 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

unknown CIF bond order: doub

unknown CIF bond order: sing

Time for openFile(*5gak): 4110 ms

reading 128975 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

128975 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

TITLE: Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome.

found biomolecule 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA

Adding embedded #jmolscript: select ({0:128954}) & connected; wireframe only;select ({128955:128974}) & !connected;stars 0.5;spacefill off;select *;

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/corescriptmath.z.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/shape/Stars.js

Script completed

Jmol script terminated

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/render/StarsRenderer.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/JV/PropertyManager.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/coreprop.z.js

-- required by JV.PropertyManager

script 2 started

antialiasDisplay = true

antialiasTranslucent = true

debugScript = false

showScript = 0

chainCaseSensitive = true

measurementUnits = "angstroms"

autobond = true

forceAutoBond = true

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/corescriptcmd.z.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/shape/Halos.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/shapesurface/Contact.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/coresurface.z.js

-- required by J.shapesurface.Contact

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/shape/MeshCollection.js

-- required by J.shapesurface.Isosurface

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/JU/XmlUtil.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/c/HB.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/JU/ContactPair.js

contact ID "hb" {environmentAtoms} hbond color TRANSLUCENT 0.2 purple;

Contact pairs: 17

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/jvxl/readers/IsoIntersectReader.js

Contacts: 4 with net volume 2.442374183127254 A^3

RasMol pseudo-hbond calculation

0 hydrogen bonds

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/core/coretext.z.js

Script completed

Jmol script terminated

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/render/HalosRenderer.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/g3d/CircleRenderer.js

s://www.ebi.ac.uk/pdbe/software/jmol-future/jsmol/j2s/J/rendersurface/ContactRenderer.js

Protein Data Bank in Europe

1 bound ligand:

1 modified residue:

Quick links

PDBe › 5gak › Ligands and Environments

1 bound ligand:

1 modified residue:

Quick links

5gak › Ligands and Environments